Background and purpose: The dynamic displacement of the carotid arteries with interference of the hyoid bone during swallowing, named as “flip-flop” phenomenon (FFP), may be associated with ischemic stroke. However, the extent to which FFP is prevalent in carotid artery disease remains unknown. We aimed to investigate its exact prevalence to explore the relationship between FFP and carotid artery disease. Methods: We examined 202 consecutive patients who were affected by neurological diseases including cerebrovascular diseases. Using carotid ultrasound, we evaluated carotid intima-media thickness, internal carotid artery stenosis (ICS), and FFP during swallowing with neck rotation. Results: FFP was observed in 39 of the 202 patients (19.3%). Patients with FFP showed significantly higher prevalence of ICS than those without FFP (12/39 [30.8] vs. 21/163 [12.9%]; p = 0.007). Among those with ICS (n = 33; 36 vessels), FFP was associated with symptomatic ICS more frequently than with asymptomatic ICS (6/11 [54.5] vs. 5/25 [20.0%]; p = 0.038). Among those with unilateral FFP (n = 37), the prevalence of ipsilateral ICS was higher than that of contralateral ICS (9/37 [24.3] vs. 2/37 [5.4%]; p = 0.035). Conclusions: FFP accompanies the swallowing movement in some neurological patients, and more frequently in patients with ICS. FFP may thus be a novel indicator of stroke.